gentry@LIFESCI.BBN.COM (Glenn Gentry) (08/04/89)
To: BIONET USERS
From: Glenn A. Gentry
Subject: BIONET'S imminent demise.
Most of you are aware that the plug will be pulled on BIONET at
the end of September, which will make problems. My interest in this
event - and the reason for this document - comes from my activities as
a virologist at the Univ. of MS Medical Center, and from my membership
on the board of OPUS, the Organization of PROPHET Users. That brings me
to the next point, which is that the PROPHET system can provide many of
the services BIONET did, plus some others that BIONET did not. (PROPHET
is a software package developed under contract for the Division of
Research Resources of NIH by BBN Systems and Technologies Corporation
located in Cambridge, MA).
Although PROPHET contains many tools (molecular modeling, curve fit-
ting, graphing, statistical analysis, and mathematical modeling) useful
to researchers in general, it also contains the following which should
be of particular interest to BIONET users:
* tools for dealing with sequence and structural databases,
including sequence retrievals and similarity searches from
either a local or centrally-maintained set of databases;
(the Baylor package MBIR is included);
* tools for dealing with macromolecular structures; and
* tools for analyzing and manipulating primary sequence data and
relating sequences to higher order structural data. (Garnier,
for example).
My personal reason for using PROPHET is that it provides a very useful
language that permits programming in the area of sequence manipulation.
In fact, just about everything in PROPHET can be done in a very broad and
comprehensive programming environment, which cannot be said about most
sequence manipulation programs (it is, however, NOT necessary to program
in order to use PROPHET; the potential is just there if you want to).
PROPHET is very inexpensive (requiring for NIH grantees only a nominal
license fee) if you have the right hardware. User support, documentation
and training services are also available for additional fees.
Hardware requirements: PROPHET runs on Sun-3 or -4 workstations, and on
a variety of DEC computers, from the Vaxstation 3000 series to Microvaxes
to the big Vaxes. They must be running UNIX (VMS WON'T work; but then UNIX
is increasing in popularity, and some say it is the operating system of
the future, at least for a research environment).
RAM and disk requirements: PROPHET needs at least 25 MB of disk space,
and at least 8MB RAM (that's a minimum figure; here, as in many - but not
all - areas of life, more is better). In a local area network, only one copy
of PROPHET need be housed; it can be accessed via the NFS tool available in
UNIX (the 8MB RAM is needed, though, at each workstation).
Because PROPHET was designed for a distributed, networked environment,
a PROPHET workstation can also provide the user with access to the larger
world of e-mail, bulletin boards, etc. (PROPHET will, however, work nicely
on a free-standing independent workstation; in such a case, however, it is
strongly recommended that a serial port and a modem be available). Access
to up-to-date versions of the PIR and of GenBank (maintained in the central
facility in Cambridge, MA) is available (via INTERNET or modem).
If you have access to the right combination of hardware, you can probably
meet most or all of your needs for molecular biology computing tools by get-
ting PROPHET; you might want to see if PROPHET is already available at your
institution. If it is not, but the hardware is, then you should contact the
person below for information about PROPHET and how to obtain it.
Dr. Richard DuBois
Biomedical Research Technology Program
Division of Research Resources
Westwood, Room 8A-15
NIH
9000 Rockville Pike
Bethesda, MD (301) 496-5411
(A recent NIH Guide (July 7, 1989, Vol 18, No. 23) contained an announcement
about PROPHET and its availability.)
I might be able to answer some questions, at least from the user's stand-
point:
Dr. Glenn A. Gentry
Department of Microbiology
Univ. of MS Medical Center
Jackson, MS 39216-4505
(601) 984-1716roy@alanine.phri.nyu.edu (Roy Smith) (08/16/90)
The "Ask Mr. Protocol" column in the August 1990 SunExpert might be
of some interest to readers of this newsgroup. The column talks about
Usenet in general this month (in its chatty sort of way), and even mentions
bionet, saying "The Bionet is a formally mananged, centrally administered
set of news-groups devoted to molecular biology." If you have access to
it, read the whole thing, it's sort of funny.
--
Roy Smith, Public Health Research Institute
455 First Avenue, New York, NY 10016
roy@alanine.phri.nyu.edu -OR- {att,cmcl2,rutgers,hombre}!phri!roy
"Arcane? Did you say arcane? It wouldn't be Unix if it wasn't arcane!"